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Yorodumi- EMDB-17841: Cryo-EM structure of Sodium proton exchanger NhaA with bound card... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17841 | |||||||||
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Title | Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Sodium proton exchanger / Cardiolipin / NhaA / TRANSPORT PROTEIN | |||||||||
Function / homology | Na+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / sodium:proton antiporter activity / regulation of pH / plasma membrane / Na(+)/H(+) antiporter NhaA Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | |||||||||
Authors | Gulati A / Meier P / Kokane S / Drew D | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin Authors: Kokane S / Meier P / Gulati A / Matsuoka R / Pipatpolkai T / Delemotte L / Drew D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17841.map.gz | 106.1 MB | EMDB map data format | |
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Header (meta data) | emd-17841-v30.xml emd-17841.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17841_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_17841.png | 104.8 KB | ||
Masks | emd_17841_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-17841.cif.gz | 5.4 KB | ||
Others | emd_17841_half_map_1.map.gz emd_17841_half_map_2.map.gz | 115.6 MB 115.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17841 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17841 | HTTPS FTP |
-Validation report
Summary document | emd_17841_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17841_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17841_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_17841_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17841 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17841 | HTTPS FTP |
-Related structure data
Related structure data | 8ps0MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17841.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.9137 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17841_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17841_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17841_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NhaA dimer
Entire | Name: NhaA dimer |
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Components |
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-Supramolecule #1: NhaA dimer
Supramolecule | Name: NhaA dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Na(+)/H(+) antiporter NhaA
Macromolecule | Name: Na(+)/H(+) antiporter NhaA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 42.304422 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPT LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI ...String: MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPT LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI IIIALFYTND LSMASLGVAA VAIAVLAVLN LCGARRTGVY ILVGVVLWTA VLKSGVHATL AGVIVGFFIP LK EKHGRSP AKRLEHVLHP WVAYLILPLF AFANAGVSLG GVTLDGLTSI LPLGIIAGML IGKPLGISLF CWLALRLKLA HLP EGTTYQ QIMVVGILCG IGFTMSIFIA SLAFGSVDPE LINWAKLGIL VGSISSAVIG YSWLRVRLRP SVGSENLYFQ UniProtKB: Na(+)/H(+) antiporter NhaA |
-Macromolecule #2: CARDIOLIPIN
Macromolecule | Name: CARDIOLIPIN / type: ligand / ID: 2 / Number of copies: 3 / Formula: CDL |
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Molecular weight | Theoretical: 1.464043 KDa |
Chemical component information | ChemComp-CDL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.11 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |